274231 Rapid Calculation of Protein Pka Values Using Rosetta

Monday, October 29, 2012: 2:40 PM
411 (Convention Center )
Krishna Praneeth Kilambi and Jeffrey J. Gray, Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD

We developed a Rosetta-based Monte Carlo method to calculate pKa values of protein residues that commonly exhibit variable protonation states (Asp, Glu, Lys, His and Tyr). We tested the technique by calculating pKa values for 270 residues from 34 proteins.  The standard Rosetta score function, which is independent of any environmental conditions, failed to capture pKa shifts. After incorporating a Coulomb electrostatic potential and optimizing the solvation reference energies for pKa calculations, a method allowing side-chain flexibility achieved a root-mean-square deviation (RMSD) of 0.83 from experimental values (0.68 after discounting 11 predictions with an error over 2 pH units). Additional degrees of side-chain conformational freedom for the proximal residues facilitated capture of charge-charge interactions in a few cases and achieved an overall RMSD of 0.85 pH units. Adding backbone flexibility increased overall RMSD to 0.94 pH units but improved relative pKa predictions for proximal catalytic residues. The method also captures large pKa shifts of lysine and some glutamate point mutations in staphylococcal nuclease. Thus, a simple and fast method based on the Rosetta score function and limited conformational sampling produces pKa values that will be useful when rapid estimation is essential, as in docking, design and folding.

Extended Abstract: File Not Uploaded
See more of this Session: Thermodynamics of Biomolecular Folding and Assembly
See more of this Group/Topical: Engineering Sciences and Fundamentals